Whole-genome sequencing reveals inter-household networks of gut-colonising ESBL-producing Escherichia coli in two rural Malawian districts
Abstract
Infection with extended-spectrum beta-lactamase-producing Escherichia coli (ESBL-Ec) is a global health concern that disproportionately affects sub-Saharan Africa. Gut mucosal colonisation is thought to precede invasive infection. Understanding ESBL-Ec colonisation and transmission across communities is therefore essential. Here, we investigate the genomic epidemiology and spatial structure of 159 gut-colonising ESBL-Ec isolates from the faeces of 211 people in two rural Malawian villages using longitudinal sampling (2023–24), whole-genome sequencing and household mapping. Colonisation prevalence rose from 34.1% (95% CI: 27.8–41.0) to 54.2% (95% CI: 46.0–62.3) over one year. Isolates belonged to 33 sequence types (STs), most commonly ST38 and ST131, harbouring 46 distinct antimicrobial resistance gene types. Fifteen strains were identified in ≥3 households that were typically separated by short geographic distances ( < 400 m). Of 190 pairwise comparisons between same-strain isolates from different households sampled concurrently within villages, 88.9% differed by ≤10 single nucleotide polymorphisms, consistent with multi-household involvement in community transmission networks. Lineage-specific ST38 and ST131 network analyses linked rural isolates to urban Malawian isolates collected within the last decade. Our findings provide a transferable framework for inferring ESBL-Ec flow in community settings and highlight the need for One Health surveillance and improved sanitation infrastructure to limit transmission.
Related
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BibTeX
@article{oferrall2026wholegenome,
title = {{Whole-genome sequencing reveals inter-household networks of gut-colonising ESBL-producing Escherichia coli in two rural Malawian districts}},
author = {Angus M. O’Ferrall and David Lally and Peter Makaula and Gladys Namacha and Joseph M. Lewis and Patrick Musicha and Richard N. Goodman and Ellie Allman and Sabrina J. Moyo and Claire S. Waddington and Sekeleghe A. Kayuni and Nicholas A. Feasey and Janelisa Musaya and J. Russell Stothard and Adam P. Roberts},
journal = {Nature Communications},
year = {2026},
month = oct,
doi = {10.1038/s41467-026-78449-1},
url = {https://www.nature.com/articles/s41467-026-78449-1},
note = {CC BY 4.0},
}
RIS
TY - JOUR
TI - Whole-genome sequencing reveals inter-household networks of gut-colonising ESBL-producing Escherichia coli in two rural Malawian districts
AU - Angus M. O’Ferrall
AU - David Lally
AU - Peter Makaula
AU - Gladys Namacha
AU - Joseph M. Lewis
AU - Patrick Musicha
AU - Richard N. Goodman
AU - Ellie Allman
AU - Sabrina J. Moyo
AU - Claire S. Waddington
AU - Sekeleghe A. Kayuni
AU - Nicholas A. Feasey
AU - Janelisa Musaya
AU - J. Russell Stothard
AU - Adam P. Roberts
PY - 2026
DA - 2026/10/14
JO - Nature Communications
DO - 10.1038/s41467-026-78449-1
UR - https://www.nature.com/articles/s41467-026-78449-1
AB - Infection with extended-spectrum beta-lactamase-producing Escherichia coli (ESBL-Ec) is a global health concern that disproportionately affects sub-Saharan Africa. Gut mucosal colonisation is thought to precede invasive infection. Understanding ESBL-Ec colonisation and transmission across communities is therefore essential. Here, we investigate the genomic epidemiology and spatial structure of 159 gut-colonising ESBL-Ec isolates from the faeces of 211 people in two rural Malawian villages using longitudinal sampling (2023–24), whole-genome sequencing and household mapping. Colonisation prevalence rose from 34.1% (95% CI: 27.8–41.0) to 54.2% (95% CI: 46.0–62.3) over one year. Isolates belonged to 33 sequence types (STs), most commonly ST38 and ST131, harbouring 46 distinct antimicrobial resistance gene types. Fifteen strains were identified in ≥3 households that were typically separated by short geographic distances ( < 400 m). Of 190 pairwise comparisons between same-strain isolates from different households sampled concurrently within villages, 88.9% differed by ≤10 single nucleotide polymorphisms, consistent with multi-household involvement in community transmission networks. Lineage-specific ST38 and ST131 network analyses linked rural isolates to urban Malawian isolates collected within the last decade. Our findings provide a transferable framework for inferring ESBL-Ec flow in community settings and highlight the need for One Health surveillance and improved sanitation infrastructure to limit transmission.
SN - 2041-1723
ER -